After merging objects: how to get rid of double faces?
As I cannot obtain any good result with the boolean (starting from Blue Fox's file), I propose this editing approach.

The steps below are in the layer #15 of the blend file : 




The objects are still separated. Open the faces to be merged.
Relocate the upper mesh and merge the two
Select the upper opposite edges and CtrlE and "bridge edge loops"
The same for the lower opposite edges
And the same for the last opened part, but without the extremities, because of the needed ngones at these extremities
Make faces for the extremities (select manually the vertices and face F)
Remove doubles


This is not a real answer of the question (more or less "how to make the boolean work"), but the job is done. No vertices were moved.

I have noticed these here :


Face centers with no face (maybe construction points ?), surrounded by O
A plane, is that printable (1) ?
And in (2), the inner faces overlap